Project Summary The focus of our laboratory is on a rare group of cancer-associated brain diseases, the "paraneoplastic neurologic disorders" (PNDs). It is believed that these patients mount an immune response against their cancers when those tumors express proteins normally restricted in their expression to neurons. These leads to the clinical phenomenon of tumor immunity and a secondary autoimmune brain disorder. One such antibody was from patients with paraneoplastic opsoclonus-myoclonus ataxia (associated with excess motor activity and lung or gynecologic tumors) to clone the targeted onconeural antigen, which we named Nova. We found that Nova is a neuron-specific RNA binding protein. In order to develop a comprehensive understanding of the function of RNA binding proteins in the brain, we developed two new methodologies in our studies of Nova. The first, termed CLIP (cross-linking immunoprecipitation), uses UV-irradiated mouse brain as a means to identify endogenous Nova-RNA complexes. The second, based in our recognition of Nova as the first identified tissue (neuron)-specific alternative splicing factor in vertebrates, used a new splicing microarray being beta-tested by Affymetrix. Here we propose to extend these studies to generate a genome-wide understanding of RNA networks that regulate alternative splicing in the brain. Our focus is on neuron- specific RNA binding proteins discovered through the study of the PNDs. In the last grant period our studies of Nova established that it is feasible to develop a complete map of RNA-protein interactions in the brain. We propose to extend the technologies developed to describe the RNA maps of the Hu PND antigens and the brPTB protein, neuron-specific RNA binding proteins. We hypothesize that both the Hu and brPTB proteins regulate alternative splicing of unique biologically coherent sets of transcripts in the mammalian brain. We will develop new methods to explore how each of these three proteins coordinately regulates RNA in the brain. Project Narrative The paraneoplastic neurologic degenerations offer unique insights into both how tumor cells can be recognized by the immune system, and how an immune response in the body can become triggered into an autoimmune attack against the brain. At the same time, the underlying biology[unreadable]why tumor cells turn on certain brain proteins, and what these proteins normally do in the brain[unreadable]is yielding new insights into how genes are regulated in special ways in the brain, and how they may be dysregulated in tumor cells.